Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000061.1 Hibiscus syriacus cultivar Beakdansim tig00000098_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 80032
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1234 original size:25 final size:24
Alignment explanation
Indices: 1200--1247 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1190 AGGGTGCTAT
1200 TTTTATAATTTTTAAAAAAA-GATAA
1 TTTTATAA--TTTAAAAAAATGATAA
*
1225 TTTTGTAATTTAAAAAAATGATA
1 TTTTATAATTTAAAAAAATGATA
1248 TTGTAGTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 4 0.19
25 7 0.33
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (24 bp):
TTTTATAATTTAAAAAAATGATAA
Found at i:1256 original size:24 final size:23
Alignment explanation
Indices: 1210--1258 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1200 TTTTATAATT
*
1210 TTTAAAAAAAGATAATTTTGTAA
1 TTTAAAAAAAGATAATTTAGTAA
1233 TTTAAAAAAATGAT-ATTGTAGTAA
1 TTTAAAAAAA-GATAATT-TAGTAA
1257 TT
1 TT
1259 ATTTTGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (23 bp):
TTTAAAAAAAGATAATTTAGTAA
Found at i:1275 original size:29 final size:29
Alignment explanation
Indices: 1243--1298 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1233 TTTAAAAAAA
1243 TGATATTGTAGTAAT-TATTTTGAAAATTG
1 TGATATTGTAGTAATGT-TTTTGAAAATTG
* *
1272 TGATATTTTGGTAATGTTTTTGAAAAT
1 TGATATTGTAGTAATGTTTTTGAAAAT
1299 GATGTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (29 bp):
TGATATTGTAGTAATGTTTTTGAAAATTG
Found at i:8403 original size:29 final size:29
Alignment explanation
Indices: 8322--8389 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
8312 ACCGTTGACC
* * *
8322 GGGTACTATTCTGGTAATTATTTGGAAAA
1 GGGTGCTATTCTAGTAATTATTTTGAAAA
*
8351 GGTTGCTATTCTAGTAATTATTTTGAAAA
1 GGGTGCTATTCTAGTAATTATTTTGAAAA
8380 GGGTGCTATT
1 GGGTGCTATT
8390 TTCATAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (29 bp):
GGGTGCTATTCTAGTAATTATTTTGAAAA
Found at i:8506 original size:29 final size:28
Alignment explanation
Indices: 8354--8506 Score: 116
Period size: 29 Copynumber: 5.5 Consensus size: 28
8344 TGGAAAAGGT
* * * * *
8354 TGCTATTCTAGTAATTATTTTGAAAAGGG
1 TGCTATTTTCGTAATT-TTTTTAAAAAGA
*
8383 TGCTATTTTCATAATTTTTTTAAAAA-A
1 TGCTATTTTCGTAATTTTTTTAAAAAGA
* *
8410 ---TAATTTCGTAATTTTTTTAAAAATA
1 TGCTATTTTCGTAATTTTTTTAAAAAGA
* * * * *
8435 TGATATTTTAGTAATTATTTTGAAAATGG
1 TGCTATTTTCGTAATT-TTTTTAAAAAGA
* *
8464 TGATATTTTGGTAATTTTTTTAAAAAAGA
1 TGCTATTTTCGTAATTTTTTT-AAAAAGA
8493 TGCTATTTTCGTAA
1 TGCTATTTTCGTAA
8507 AATGGTTGTT
Statistics
Matches: 98, Mismatches: 20, Indels: 12
0.75 0.15 0.09
Matches are distributed among these distances:
24 21 0.21
25 1 0.01
28 23 0.23
29 53 0.54
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.48
Consensus pattern (28 bp):
TGCTATTTTCGTAATTTTTTTAAAAAGA
Found at i:17328 original size:75 final size:75
Alignment explanation
Indices: 17196--17337 Score: 212
Period size: 75 Copynumber: 1.9 Consensus size: 75
17186 AACAGTTTGT
* ** * * *
17196 AAGTTTATAAAGAATGAGATAATTTGATTATATGAGTTTCTAGAGAGCATTTTTAACAAACTAAT
1 AAGTTTATAAAGAAGGAGATAATTTGACGATATGAGTTTCTAAAAAGCATTTGTAACAAACTAAT
17261 CTAATACGAC
66 CTAATACGAC
* *
17271 AAGTTTATAAAGAAGGAGCTAATTTGACGATATGAGTTTCTAAAAAGGATTTGTAACAAACTAAT
1 AAGTTTATAAAGAAGGAGATAATTTGACGATATGAGTTTCTAAAAAGCATTTGTAACAAACTAAT
17336 CT
66 CT
17338 GACACAACAC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 59 1.00
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (75 bp):
AAGTTTATAAAGAAGGAGATAATTTGACGATATGAGTTTCTAAAAAGCATTTGTAACAAACTAAT
CTAATACGAC
Found at i:29060 original size:29 final size:29
Alignment explanation
Indices: 29018--29169 Score: 144
Period size: 29 Copynumber: 5.2 Consensus size: 29
29008 CATACATTCT
* *
29018 TGATTTTGCATGAGATTATATCTCAC-TCC
1 TGATTCTGCATGGGATTATATCTC-CGTCC
* * *
29047 TGATTCTGCATGAGATTATATCACCGTCT
1 TGATTCTGCATGGGATTATATCTCCGTCC
* * *
29076 TGATTCTACATGGGATTGTATCTCCTTCC
1 TGATTCTGCATGGGATTATATCTCCGTCC
** **
29105 TGATTCTATATGGGATTATATCTTTGTCC
1 TGATTCTGCATGGGATTATATCTCCGTCC
* * *
29134 TAATTCTGCATGGGAGTATATCCCCGTCC
1 TGATTCTGCATGGGATTATATCTCCGTCC
*
29163 TGTTTCT
1 TGATTCT
29170 ATTTGCTTCA
Statistics
Matches: 99, Mismatches: 23, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
28 1 0.01
29 98 0.99
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.41
Consensus pattern (29 bp):
TGATTCTGCATGGGATTATATCTCCGTCC
Found at i:32291 original size:23 final size:22
Alignment explanation
Indices: 32265--32307 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
32255 ATAAAAAATA
32265 TATTTTTTATTAAATATTTTTGG
1 TATTTTTTATTAAAT-TTTTTGG
*
32288 TATTTTTTATTTAATTTTTT
1 TATTTTTTATTAAATTTTTT
32308 AAATAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (22 bp):
TATTTTTTATTAAATTTTTTGG
Found at i:33443 original size:28 final size:29
Alignment explanation
Indices: 33397--33464 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 29
33387 TGTATTTCCT
*
33397 TCCTGATTCTACATGAGATTACATCC-CG
1 TCCTGATTCTACATAAGATTACATCCTCG
*
33425 TCCTGATTCTGCATAAGATTACATCCTCG
1 TCCTGATTCTACATAAGATTACATCCTCG
* *
33454 TCGTGTTTCTA
1 TCCTGATTCTA
33465 TATGGGGTCC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 24 0.71
29 10 0.29
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (29 bp):
TCCTGATTCTACATAAGATTACATCCTCG
Found at i:36411 original size:24 final size:24
Alignment explanation
Indices: 36384--36431 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
36374 ATTTTGTGTA
*
36384 ATGTCATACTGTCTTTACTATCCC
1 ATGTCATACTGCCTTTACTATCCC
36408 ATGTCATACTGCCTTTACTATCCC
1 ATGTCATACTGCCTTTACTATCCC
36432 GACTAAGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.31, G:0.08, T:0.40
Consensus pattern (24 bp):
ATGTCATACTGCCTTTACTATCCC
Found at i:38309 original size:63 final size:63
Alignment explanation
Indices: 38210--38335 Score: 180
Period size: 63 Copynumber: 2.0 Consensus size: 63
38200 TTGTTAAAAG
* * *
38210 GGGTAAACTTCATTTTGGCTCCCTATGTTCTGAAAAACATTCAATTTGGTCCCCAAACCGGTT
1 GGGTAAACTTCATTTTGGCTCCCTATATTCTAAAAAACATTCAATTCGGTCCCCAAACCGGTT
* * * * *
38273 GGGTAAACTTCATTTTGGCTCCCTCTATTTTAAAAAACGTTTAATTCGGTCCCCAAATCGGTT
1 GGGTAAACTTCATTTTGGCTCCCTATATTCTAAAAAACATTCAATTCGGTCCCCAAACCGGTT
38336 TAATTCCCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (63 bp):
GGGTAAACTTCATTTTGGCTCCCTATATTCTAAAAAACATTCAATTCGGTCCCCAAACCGGTT
Found at i:49506 original size:1 final size:1
Alignment explanation
Indices: 49471--49498 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
49461 TCTTAAGTTG
49471 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
49499 GAGAAAAACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:50667 original size:106 final size:105
Alignment explanation
Indices: 50297--50775 Score: 750
Period size: 105 Copynumber: 4.7 Consensus size: 105
50287 AGGTTTTACC
50297 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
50362 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
50402 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
50467 ATGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
50507 CAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
50572 ACGAAGGGACCGCTGCTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* *
50613 CAGAGCCAATTTCAACGTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
50678 ACGAAGGGACCGCTGGTTGTCAA-TAA-A-----CAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
50711 C----CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTAC-C-AGTTCAACTTCA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA--ACGCAAGTTCAACTTCA
50770 CGACGA
64 CGACGA
50776 GGATGTCACT
Statistics
Matches: 357, Mismatches: 14, Indels: 17
0.92 0.04 0.04
Matches are distributed among these distances:
94 57 0.16
95 1 0.00
96 2 0.01
98 7 0.02
103 1 0.00
105 195 0.55
106 94 0.26
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:50697 original size:211 final size:203
Alignment explanation
Indices: 50297--50775 Score: 736
Period size: 211 Copynumber: 2.3 Consensus size: 203
50287 AGGTTTTACC
*
50297 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
* * *
50362 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGCTTGTCAACAAACACTTCTCAATTTCAGAGCCAATTTCAACGTCACAACG
** *
50427 AAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACA
131 AAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-A
50492 AACATTTCTCAATTT
195 AA-A-----CAATTT
*
50507 CAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
50572 ACGAAGGGACCGCTGCTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACGTCACAAC
66 ACGAAGGGACCGCTGCTTGTCAACAAAC-ACTTCTCAATTTCAGAGCCAATTTCAACGTCACAAC
*
50637 GAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT
130 GAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAA
50702 AAACAATTT
195 AAACAATTT
*
50711 C----CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGAC-A-GTACCAGTTCAACTTCA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTA--AGTTCAACTTCA
50770 CGACGA
64 CGACGA
50776 GGATGTCACT
Statistics
Matches: 255, Mismatches: 11, Indels: 16
0.90 0.04 0.06
Matches are distributed among these distances:
198 3 0.01
199 1 0.00
200 56 0.22
204 7 0.03
209 1 0.00
210 92 0.36
211 95 0.37
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (203 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGCTTGTCAACAAACACTTCTCAATTTCAGAGCCAATTTCAACGTCACAACG
AAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAA
AACAATTT
Found at i:52090 original size:63 final size:62
Alignment explanation
Indices: 51977--52101 Score: 169
Period size: 63 Copynumber: 2.0 Consensus size: 62
51967 TTGTTAAAAG
* * *
51977 GGGTAAACTTCATTTGGCTCCCTATGTTCTGAAAAACATTCAATTTGGTCCCCAAACCGGTT
1 GGGTAAACTTCATTTGGCTCCCTATATTCTAAAAAACATTCAATTCGGTCCCCAAACCGGTT
* * * * *
52039 GGGTAAACTTCATTTTGGCTCCCTCTATTTTAAAAAACGTTTAATTCGGTCCCCAAATCGGTT
1 GGGTAAACTTCA-TTTGGCTCCCTATATTCTAAAAAACATTCAATTCGGTCCCCAAACCGGTT
52102 TAATTCCCTT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
62 12 0.22
63 42 0.78
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (62 bp):
GGGTAAACTTCATTTGGCTCCCTATATTCTAAAAAACATTCAATTCGGTCCCCAAACCGGTT
Found at i:52598 original size:2 final size:2
Alignment explanation
Indices: 52591--52629 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
52581 TTATATTTTA
* * *
52591 AT AT AT AT GT AT AT AT AT AT AT AT AT AT CT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
52630 CTTGTAATAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52635 original size:10 final size:12
Alignment explanation
Indices: 52591--52667 Score: 58
Period size: 12 Copynumber: 6.8 Consensus size: 12
52581 TTATATTTTA
*
52591 ATATATATGTAT
1 ATATCTATGTAT
* *
52603 ATATATATATAT
1 ATATCTATGTAT
52615 ATATCTATGTAT
1 ATATCTATGTAT
52627 ATA-CT-TGTA-
1 ATATCTATGTAT
* *
52636 ATAGTTTATTTAT
1 ATA-TCTATGTAT
52649 ATATCTAT-TAT
1 ATATCTATGTAT
52660 -TAT-TATGT
1 ATATCTATGT
52668 GTACATTTCA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
9 6 0.11
10 8 0.15
11 6 0.11
12 31 0.57
13 3 0.06
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.53
Consensus pattern (12 bp):
ATATCTATGTAT
Found at i:53329 original size:23 final size:23
Alignment explanation
Indices: 53277--53330 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
53267 CTATTAATAC
*
53277 ATATAACCACTAAAAGTTTGATA
1 ATATAATCACTAAAAGTTTGATA
53300 ATATAATCACTAAAAGTTTGATA
1 ATATAATCACTAAAAGTTTGATA
*
53323 TTATAATC
1 ATATAATC
53331 TGATATCCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.35
Consensus pattern (23 bp):
ATATAATCACTAAAAGTTTGATA
Found at i:55888 original size:49 final size:49
Alignment explanation
Indices: 55809--55905 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 49
55799 TGTTGCTATA
*
55809 ACAATATCAAACTTTGATGAGTTATCTGTTGCCACAACATTGCCTTGAC
1 ACAATATCAAACTTTGATGAATTATCTGTTGCCACAACATTGCCTTGAC
* **
55858 ACAATATCAAACTTTGATGAATTATTTGTTGCTGCAACATTGCCTTGA
1 ACAATATCAAACTTTGATGAATTATCTGTTGCCACAACATTGCCTTGA
55906 TACGCGGATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (49 bp):
ACAATATCAAACTTTGATGAATTATCTGTTGCCACAACATTGCCTTGAC
Found at i:60984 original size:9 final size:9
Alignment explanation
Indices: 60972--60997 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
60962 AATAAATATT
60972 AATAATAAC
1 AATAATAAC
60981 AATAATAAC
1 AATAATAAC
60990 AATAATAA
1 AATAATAA
60998 ATAAAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (9 bp):
AATAATAAC
Found at i:61483 original size:131 final size:128
Alignment explanation
Indices: 61331--61710 Score: 344
Period size: 131 Copynumber: 2.9 Consensus size: 128
61321 TATATGAAAA
* * * *
61331 TTTGATTCACTTCACTGCTCTTTAAGGATAGTTAAATCGAGGTAGATTTGATCCACCACTCTTCA
1 TTTGATTC-CTTCACTGCTCTTCAAGGATAGTTGAATCGAGGTAGATTTGCTCCACTACTCTTCA
* * * *
61396 AAGGATATCAAATTTGGAAATGGGATTTG-TCTCGTTACACTTTAGGGGAGATCAAAACT-GGTA
65 AAGGA-ATCAAATTTGGAAATGAGATTTGCTCT-GCTACACTTTAGGGAAGATCAAAACTAAG--
61459 ACT
126 ACT
* * * * *
61462 TTTGATTCGCTTCACTGCTCTTCAAGGA-AGATTGAATTGAGGTATATTTTCTCCATTGCTCTTC
1 TTTGATTC-CTTCACTGCTCTTCAAGGATAG-TTGAATCGAGGTAGATTTGCTCCACTACTCTTC
* * * * *
61526 AAGAAGG-ATCAAATCTGGAAATGAGATTTGCTCTGCTACTCTTTAGGGAAGATTAGACCTAAGA
64 -A-AAGGAATCAAATTTGGAAATGAGATTTGCTCTGCTACACTTTAGGGAAGATCAAAACTAAGA
61590 CT
127 CT
* * *
61592 TTTGATT-ATTGCACTACTCTTCAAGGAATA-TTGAATCGAGGTAGATTTGCTCCACTACTTTTC
1 TTTGATTCCTT-CACTGCTCTTCAAGG-ATAGTTGAATCGAGGTAGATTTGCTCCACTACTCTTC
* * * *
61655 AAAGAAGATCAAATATTGGAAGAATG-GATCTGCTGTGCTATACTTTA-GGAAGATCA
64 AAAGGA-ATCAAAT-TTGG-A-AATGAGATTTGCTCTGCTACACTTTAGGGAAGATCA
61711 GACGGCTTAT
Statistics
Matches: 202, Mismatches: 34, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
127 3 0.01
128 3 0.01
129 48 0.24
130 24 0.12
131 111 0.55
132 9 0.04
133 4 0.02
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34
Consensus pattern (128 bp):
TTTGATTCCTTCACTGCTCTTCAAGGATAGTTGAATCGAGGTAGATTTGCTCCACTACTCTTCAA
AGGAATCAAATTTGGAAATGAGATTTGCTCTGCTACACTTTAGGGAAGATCAAAACTAAGACT
Found at i:66808 original size:14 final size:14
Alignment explanation
Indices: 66789--66818 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
66779 ACTGAAAAGG
66789 AGTATCGATACCAT
1 AGTATCGATACCAT
66803 AGTATCGATACCAT
1 AGTATCGATACCAT
66817 AG
1 AG
66819 GAGGGGTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (14 bp):
AGTATCGATACCAT
Found at i:67232 original size:54 final size:54
Alignment explanation
Indices: 67148--67435 Score: 404
Period size: 54 Copynumber: 5.4 Consensus size: 54
67138 GCATTTACCC
* *
67148 TATTGGAACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCG
1 TATTGGCACTATGTGTGCAACCTAATAAATTCATAATAAGTTTATGAATTTTCG
* *
67202 AATTGGCACTATGTGTGCAACCCAATAAATTCATAATAA-TTTATGAA-TTTCTG
1 TATTGGCACTATGTGTGCAACCTAATAAATTCATAATAAGTTTATGAATTTTC-G
* * * *
67255 TATTGACACTATGTGTGCAACCTAAGAAATTTATAATAAGTGTATGAATTTTCG
1 TATTGGCACTATGTGTGCAACCTAATAAATTCATAATAAGTTTATGAATTTTCG
* *
67309 TATTGGCAGTATGTGTGCAACCT-ATGAAATTCATAATAAGTTTATG-ATTTTCAA
1 TATTGGCACTATGTGTGCAACCTAAT-AAATTCATAATAAGTTTATGAATTTTC-G
* * *
67363 TATTGGCATTATGTGCGCAACCTAATAAATTCATAATTAGTTTATGAATTTTCG
1 TATTGGCACTATGTGTGCAACCTAATAAATTCATAATAAGTTTATGAATTTTCG
67417 TATTGGCACTATGTGTGCA
1 TATTGGCACTATGTGTGCA
67436 CGTTTGTGAA
Statistics
Matches: 205, Mismatches: 22, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
52 4 0.02
53 50 0.24
54 139 0.68
55 12 0.06
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.38
Consensus pattern (54 bp):
TATTGGCACTATGTGTGCAACCTAATAAATTCATAATAAGTTTATGAATTTTCG
Found at i:67339 original size:107 final size:108
Alignment explanation
Indices: 67155--67435 Score: 422
Period size: 107 Copynumber: 2.6 Consensus size: 108
67145 CCCTATTGGA
*
67155 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGAATTGGCACTATGTGTGC
1 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGC
**
67220 AACCCAATAAATTCATAATAA-TTTATGAATTTCTGTATTGAC
66 AACCCAATAAATTCATAATAAGTTTATGAATTTCAATATTGAC
* * *
67262 ACTATGTGTGCAACCTAAGAAATTTATAATAAGTGTATGAATTTTCGTATTGGCAGTATGTGTGC
1 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGC
* * *
67327 AA-CCTATGAAATTCATAATAAGTTTATGATTTTCAATATTGGC
66 AACCCAAT-AAATTCATAATAAGTTTATGAATTTCAATATTGAC
* * * *
67370 ATTATGTGCGCAACCTAATAAATTCATAATTAGTTTATGAATTTTCGTATTGGCACTATGTGTGC
1 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGC
67435 A
66 A
67436 CGTTTGTGAA
Statistics
Matches: 156, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
106 4 0.03
107 76 0.49
108 76 0.49
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (108 bp):
ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGC
AACCCAATAAATTCATAATAAGTTTATGAATTTCAATATTGAC
Found at i:67453 original size:35 final size:35
Alignment explanation
Indices: 67402--67469 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
67392 TTCATAATTA
* * * *
67402 GTTTATGAATTTTCGTATTGGCACTATGTGTGCAC
1 GTTTATGAATTATCGTATCGGCAATACGTGTGCAC
*
67437 GTTTGTGAATTATCGTATCGGCAATACGTGTGC
1 GTTTATGAATTATCGTATCGGCAATACGTGTGC
67470 GAAAACCACT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.40
Consensus pattern (35 bp):
GTTTATGAATTATCGTATCGGCAATACGTGTGCAC
Found at i:69961 original size:20 final size:19
Alignment explanation
Indices: 69936--69985 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
69926 GATTCAATCT
*
69936 GTATCGATACAGAAGGG-GG
1 GTATCGATAC-GAAGGGAAG
69955 AGTATCGATATCGAAGGGAAG
1 -GTATCGATA-CGAAGGGAAG
69976 GTATCGATAC
1 GTATCGATAC
69986 CATTAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 1 0.04
20 24 0.89
21 2 0.07
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (19 bp):
GTATCGATACGAAGGGAAG
Found at i:70077 original size:20 final size:21
Alignment explanation
Indices: 70011--70081 Score: 76
Period size: 22 Copynumber: 3.5 Consensus size: 21
70001 TGCAAAAATG
* *
70011 GTATCAATACCATAGCAT--A
1 GTATCGATACCATAGTATGGA
*
70030 GTATCGGTACCATAGTATGGTA
1 GTATCGATACCATAGTATGG-A
*
70052 GTATCGATACCATGGTATGG-
1 GTATCGATACCATAGTATGGA
70072 GTATCGATAC
1 GTATCGATAC
70082 TGAGGAGCCA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
19 15 0.34
20 10 0.23
22 19 0.43
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.30
Consensus pattern (21 bp):
GTATCGATACCATAGTATGGA
Found at i:70545 original size:45 final size:45
Alignment explanation
Indices: 70476--70567 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
70466 AACAAATGAA
* *
70476 CAAAATAATATTGCATATGGGTGCATTATCGGCATGAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGGCATAAAAGGATGC
* *
70521 CAAAATAATAATGCATATGTGTGCATTATTGGCATAAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGGCATAAAAGGATGC
70566 CA
1 CA
70568 TAGTTGAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (45 bp):
CAAAATAATAATGCATATGGGTGCATTATCGGCATAAAAGGATGC
Found at i:76686 original size:22 final size:22
Alignment explanation
Indices: 76627--76687 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
76617 TGCAAAAATG
*
76627 GTATCGATACCATAGCA---TA
1 GTATCGATACCATAGTATGGTA
* *
76646 GTATCGGTACCATATTATGGTA
1 GTATCGATACCATAGTATGGTA
*
76668 GTATCGATACCATGGTATGG
1 GTATCGATACCATAGTATGG
76688 GTACCGATAC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 14 0.42
22 19 0.58
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (22 bp):
GTATCGATACCATAGTATGGTA
Found at i:77164 original size:45 final size:45
Alignment explanation
Indices: 77103--77235 Score: 214
Period size: 45 Copynumber: 3.0 Consensus size: 45
77093 AATGAATGAA
*
77103 CAAAATAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
1 CAAAATAATAAAGCATATGGGTGCATTATCGGCATGAAAGGATGC
*
77148 CAAAATAACAAAGCATACT-GGTGCATTATCGGCATGAAAGGATGC
1 CAAAATAATAAAGCATA-TGGGTGCATTATCGGCATGAAAGGATGC
* *
77193 CAAAATAATAACGCATATGGGTGCATTATTGGCATGAAAGGAT
1 CAAAATAATAAAGCATATGGGTGCATTATCGGCATGAAAGGAT
77236 ACCATAGTTG
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
44 1 0.01
45 79 0.98
46 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.23
Consensus pattern (45 bp):
CAAAATAATAAAGCATATGGGTGCATTATCGGCATGAAAGGATGC
Found at i:77254 original size:45 final size:45
Alignment explanation
Indices: 77103--77267 Score: 208
Period size: 45 Copynumber: 3.7 Consensus size: 45
77093 AATGAATGAA
*
77103 CAAAATAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
1 CAAAATAACAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
*
77148 CAAAATAACAAAGCATACT-GGTGCATTATCGGCATGAAAGGATGC
1 CAAAATAACAATGCATA-TGGGTGCATTATCGGCATGAAAGGATGC
* * * *
77193 CAAAATAATAACGCATATGGGTGCATTATTGGCATGAAAGGATAC
1 CAAAATAACAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
** * *
77238 CATAGTTGA-AATGCATATGTGTGCATTATC
1 CA-AAATAACAATGCATATGGGTGCATTATC
77268 AACATAAAAG
Statistics
Matches: 105, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
44 1 0.01
45 100 0.95
46 4 0.04
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (45 bp):
CAAAATAACAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
Found at i:77254 original size:90 final size:90
Alignment explanation
Indices: 77103--77267 Score: 235
Period size: 90 Copynumber: 1.8 Consensus size: 90
77093 AATGAATGAA
* *
77103 CAAAATAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCAAAATAACAAAGCATACTG
1 CAAAATAATAACGCATATGGGTGCATTATCGGCATGAAAGGATACCAAAATAACAAAGCATA-TG
77168 -GTGCATTATCGGCATGAAAGGATGC
65 TGTGCATTATCGGCATGAAAGGATGC
* ** * *
77193 CAAAATAATAACGCATATGGGTGCATTATTGGCATGAAAGGATACCATAGTTGA-AATGCATATG
1 CAAAATAATAACGCATATGGGTGCATTATCGGCATGAAAGGATACCA-AAATAACAAAGCATATG
77257 TGTGCATTATC
65 TGTGCATTATC
77268 AACATAAAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
89 2 0.03
90 61 0.92
91 3 0.05
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (90 bp):
CAAAATAATAACGCATATGGGTGCATTATCGGCATGAAAGGATACCAAAATAACAAAGCATATGT
GTGCATTATCGGCATGAAAGGATGC
Found at i:78938 original size:46 final size:46
Alignment explanation
Indices: 78863--78963 Score: 139
Period size: 46 Copynumber: 2.2 Consensus size: 46
78853 ACAAATCCAT
* ** *
78863 AAATGAAATGCATGAAATAATGTACTAAGGCATGAAAGGATGCCAC
1 AAATGAAATGCATGAAAGAATACACTAAGGCATAAAAGGATGCCAC
* * *
78909 AAATGAAATGCATGAAAGGATACATTAAGGCATAAAAGGATGCCAT
1 AAATGAAATGCATGAAAGAATACACTAAGGCATAAAAGGATGCCAC
78955 AAATGAAAT
1 AAATGAAAT
78964 TAATGAATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.49, C:0.11, G:0.21, T:0.20
Consensus pattern (46 bp):
AAATGAAATGCATGAAAGAATACACTAAGGCATAAAAGGATGCCAC
Done.